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Aurzada F, Betz V, Lifshits M. Breaking a chain of interacting Brownian particles. ANN APPL PROBAB 2021. [DOI: 10.1214/20-aap1658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Frank Aurzada
- Fachbereich Mathematik, Technische Universität Darmstadt
| | - Volker Betz
- Fachbereich Mathematik, Technische Universität Darmstadt
| | - Mikhail Lifshits
- Department of Mathematics and Computer Science, St. Petersburg State University
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2
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Elias-Mordechai M, Chetrit E, Berkovich R. Interplay between Viscoelasticity and Force Rate Affects Sequential Unfolding in Polyproteins Pulled at Constant Velocity. Macromolecules 2020; 53:3021-3029. [PMID: 32905266 PMCID: PMC7467765 DOI: 10.1021/acs.macromol.0c00278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/30/2020] [Indexed: 11/30/2022]
Abstract
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Polyproteins are
unique constructs, comprised of folded protein
domains in tandem and polymeric linkers. These macromolecules perform
under biological stresses by modulating their response through partial
unfolding and extending. Although these unfolding events are considered
independent, a history dependence of forced unfolding within polyproteins
was reported. Here we measure the unfolding of single poly(I91) octamers,
complemented with Brownian dynamics simulations, displaying increasing
hierarchy in unfolding-foces, accompanied by a decrease in the effective
stiffness. This counters the existing understanding that relates stiffness
with variations in domain size and probe stiffness, which is expected
to reduce the unfolding forces with every consecutive unfolding event.
We utilize a simple mechanistic viscoelastic model to show that two
effects are combined within a sequential forced unfolding process:
the viscoelastic properties of the growing linker chain lead to a
hierarchy of the unfolding events, and force-rate application governs
the unfolding kinetics.
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Affiliation(s)
- Moran Elias-Mordechai
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Einat Chetrit
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ronen Berkovich
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.,The Ilze Katz Institute for Nanoscience and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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3
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Engel MC, Smith DM, Jobst MA, Sajfutdinow M, Liedl T, Romano F, Rovigatti L, Louis AA, Doye JPK. Force-Induced Unravelling of DNA Origami. ACS NANO 2018; 12:6734-6747. [PMID: 29851456 DOI: 10.1021/acsnano.8b01844] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently proposed origami biosensor, whose function takes advantage of origami behavior under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inward for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces and what design principles can be applied to enhance stability.
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Affiliation(s)
- Megan C Engel
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Perlickstraβe 1 , 04103 Leipzig , Germany
| | - Markus A Jobst
- Department für Physik , Ludwig-Maximilians-Universität Amalienstrasse 54 80799 München , Germany
| | - Martin Sajfutdinow
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Perlickstraβe 1 , 04103 Leipzig , Germany
| | - Tim Liedl
- Department für Physik , Ludwig-Maximilians-Universität Amalienstrasse 54 80799 München , Germany
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi , Università Ca' Foscari di Venezia , Via Torino 155 , 30172 Venezia Mestre , Italy
| | - Lorenzo Rovigatti
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
- CNR-ISC , Uos Sapienza, Piazzale A. Moro 2 , 00185 Roma , Italy
- Dipartimento di Fisica , Sapienza Università di Roma , Piazzale A. Moro 2 , 00185 Roma , Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
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Bullerjahn JT, Sturm S, Kroy K. Theory of rapid force spectroscopy. Nat Commun 2014; 5:4463. [PMID: 25079911 PMCID: PMC4124868 DOI: 10.1038/ncomms5463] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/19/2014] [Indexed: 12/19/2022] Open
Abstract
In dynamic force spectroscopy, single (bio-)molecular bonds are actively broken to assess their range and strength. At low loading rates, the experimentally measured statistical distributions of rupture forces can be analysed using Kramers’ theory of spontaneous unbinding. The essentially deterministic unbinding events induced by the extreme forces employed to speed up full-scale molecular simulations have been interpreted in mechanical terms, instead. Here we start from a rigorous probabilistic model of bond dynamics to develop a unified systematic theory that provides exact closed-form expressions for the rupture force distributions and mean unbinding forces, for slow and fast loading protocols. Comparing them with Brownian dynamics simulations, we find them to work well also at intermediate pulling forces. This renders them an ideal companion to Bayesian methods of data analysis, yielding an accurate tool for analysing and comparing force spectroscopy data from a wide range of experiments and simulations. Dynamic force spectroscopy is widely applied to probe molecular interactions by forcible bond breaking, but it currently lacks an analytical theory that spans the divide between experiment and simulation. Here, such a unified framework is developed and shown to be accurate for slow and fast loading.
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Affiliation(s)
- Jakob T Bullerjahn
- Universität Leipzig, Institut für theoretische Physik, 04103 Leipzig, Germany
| | - Sebastian Sturm
- Universität Leipzig, Institut für theoretische Physik, 04103 Leipzig, Germany
| | - Klaus Kroy
- Universität Leipzig, Institut für theoretische Physik, 04103 Leipzig, Germany
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5
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Froltsov VA, Klüppel M, Raos G. Molecular dynamics simulation of rupture in glassy polymer bridges within filler aggregates. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:041801. [PMID: 23214604 DOI: 10.1103/physreve.86.041801] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 07/25/2012] [Indexed: 06/01/2023]
Abstract
We present a series of nonequilibrium molecular dynamics simulations, investigating the rupture mechanisms in glassy polymer films confined between two solid surfaces. Such systems provide a useful model for the strong nonlinear reinforcement of rubber by colloidal filler particles. Depending on the degree of confinement three qualitatively different rupture modes have been found, which originate from the interplay of internal (polymer-polymer) and external (polymer-wall) interactions. In very thin films we observe the formation and stretching of many single-chain bridges between the confining surfaces. Progressing to thicker samples we observe fewer bridges, consisting of bundled polymer chains, and eventually just one large bridge in thick specimens. The yield stress and the elongational modulus of the polymer films have been calculated from the stress-strain curves at various temperatures and confinements and their behavior has been analyzed in terms of polymer-polymer and polymer-surface interaction energies. The thinnest films (5 monomer diameters) are always glassy in our simulations, while the others display a glass transition temperature around 0.50-0.55 (in units ε(0)/k(B) of the Lennard-Jones interaction energy), depending on their thickness. This range of values, which has been determined using both the nonequilibrium tensile simulations and equilibrium diffusion data, agrees with the transition temperature previously found by shear simulations [Baljon and Robbins, Science 271, 482 (1996)].
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Affiliation(s)
- Vladimir A Froltsov
- Deutsches Institut für Kautschuktechnologie e.V., Eupener Strasse 33, D-30519 Hannover, Germany
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Embrechts A, Schönherr H, Vancso GJ. Forced Unbinding of Individual Urea–Aminotriazine Supramolecular Polymers by Atomic Force Microscopy: A Closer Look at the Potential Energy Landscape and Binding Lengths at Fixed Loading Rates. J Phys Chem B 2011; 116:565-70. [DOI: 10.1021/jp2089752] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Anika Embrechts
- Department of Materials Science and Technology of Polymers and MESA+ Institute for Nanotechnology, University of Twente, Post Office Box 217, 7500 AE Enschede, The Netherlands
| | - Holger Schönherr
- Department of Materials Science and Technology of Polymers and MESA+ Institute for Nanotechnology, University of Twente, Post Office Box 217, 7500 AE Enschede, The Netherlands
| | - G. Julius Vancso
- Department of Materials Science and Technology of Polymers and MESA+ Institute for Nanotechnology, University of Twente, Post Office Box 217, 7500 AE Enschede, The Netherlands
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8
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Ghosh A, Dimitrov DI, Rostiashvili VG, Milchev A, Vilgis TA. Thermal breakage and self-healing of a polymer chain under tensile stress. J Chem Phys 2010; 132:204902. [DOI: 10.1063/1.3427245] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Bhattacharya A, Binder K. Out-of-equilibrium characteristics of a forced translocating chain through a nanopore. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:041804. [PMID: 20481741 DOI: 10.1103/physreve.81.041804] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Indexed: 05/29/2023]
Abstract
Polymer translocation through a nanopore in a thin membrane is studied using a coarse-grained bead-spring model and Langevin dynamics simulation with a particular emphasis to explore out of equilibrium characteristics of the translocating chain. We analyze the out of equilibrium chain conformations both at the cis and the trans side separately either as a function of the time during the translocation process or as as function of the monomer index m inside the pore. A detailed picture of translocation emerges by monitoring the center of mass of the translocating chain, longitudinal and transverse components of the gyration radii and the end to end vector. We observe that polymer configurations at the cis side are distinctly different from those at the trans side. During the translocation and immediately afterwards, the chain is clearly out of equilibrium, as different parts of the chain are characterized by a series of effective Flory exponents. We further notice that immediately after the translocation the last set of beads that have just translocated take a relatively compact structure compared to the first set of beads that translocated earlier and the chain immediately after translocation is described by an effective Flory exponent 0.45+/-0.01. The analysis of these results is further strengthened by looking at the conformations of chain segments of equal length as they cross from the cis to the trans side, We discuss implications of these results to the theoretical estimates and numerical simulation studies of the translocation exponent reported by various groups.
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Affiliation(s)
- Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA.
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